aignostics 0.2.0__tar.gz → 0.2.1__tar.gz

{aignostics-0.2.0 → aignostics-0.2.1}/PKG-INFO

@@ -1,12 +1,13 @@
 Metadata-Version: 2.4
 Name: aignostics
-Version: 0.2.0
+Version: 0.2.1
 Summary: 🔬 Python SDK providing access to Aignostics AI services.
 Project-URL: Homepage, https://aignostics.readthedocs.io/en/latest/
 Project-URL: Documentation, https://aignostics.readthedocs.io/en/latest/
 Project-URL: Source, https://github.com/aignostics/python-sdk
 Project-URL: Changelog, https://github.com/aignostics/python-sdk/releases
 Project-URL: Issues, https://github.com/aignostics/python-sdk/issues
+Author: Andreas Kuhn
 Author-email: Helmut Hoffer von Ankershoffen <helmut@aignostics.com>
 License: MIT License
         
@@ -30,7 +31,7 @@ License: MIT License
         OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
         SOFTWARE.
 License-File: LICENSE
-Keywords: act,aignostics,codecov,copier,cyclonedx,detect-secrets,devcontainer,docker,git-cliff,jupyter,marimo,mypy,nicegui,nox,oe-python-template,pip-audit,pip-licenses,pre-commit,pydantic,pypi,pytest,python,readthedocs,ruff,sonarcloud,sonarqube,sphinx,streamlit,typer,uv
+Keywords: act,aignostics,atlas,codecov,copier,cyclonedx,detect-secrets,devcontainer,dicom,digital-pathology,docker,git-cliff,image-data-commons,jupyter,machine-learning,marimo,medical-imaging,mypy,nicegui,nox,oe-python-template,openslide,pip-audit,pip-licenses,pre-commit,pydantic,pydicom,pypi,pytest,python,qupath,readthedocs,ruff,sonarcloud,sonarqube,sphinx,typer,uv,whole-slide-imaging
 Classifier: Development Status :: 3 - Alpha
 Classifier: Framework :: Pydantic
 Classifier: Framework :: Pytest
@@ -105,7 +106,7 @@ Provides-Extra: jupyter
 Requires-Dist: jupyter>=1.1.1; extra == 'jupyter'
 Provides-Extra: marimo
 Requires-Dist: cloudpathlib>=0.21.1; extra == 'marimo'
-Requires-Dist: marimo>=0.13.10; extra == 'marimo'
+Requires-Dist: marimo>=0.13.11; extra == 'marimo'
 Requires-Dist: matplotlib>=3.10.3; extra == 'marimo'
 Requires-Dist: shapely>=2.1.0; extra == 'marimo'
 Provides-Extra: qupath
@@ -130,7 +131,8 @@ Description-Content-Type: text/markdown
 [![Uptime](https://uptime.betterstack.com/status-badges/v2/monitor/1wbqa.svg)](https://aignostics.betteruptime.com)
 
 > [!NOTE]
-> This project is currently in alpha phase. Watch or star the repository to stay updated on its progress.
+> The Aignostics Python SDK is in alpha, with [Atlas H&E-TME](https://www.aignostics.com/products/he-tme-profiling-product) running on the [Aignostics Platform](https://platform.aignostics.com) being in [early access](https://www.linkedin.com/posts/aignostics_introducing-atlas-he-tme-aignostics-is-activity-7325865745827979265-Sya9?utm_source=share&utm_medium=member_desktop&rcm=ACoAABRmV7cBCGv8eM_ot_kRTrBsb12olQvoLS4). 
+> Watch or star this repository to receive updates on new features and improvements of the Aignostics Python SDK.
 
 ---
 
@@ -140,19 +142,17 @@ Description-Content-Type: text/markdown
 The Aignostics Python SDK includes multiple pathways to interact with the
 Aignostics Platform:
 
-1. Use the **Aignostics Launchpad** to analyze your whole slide images 
-   with our AI applications and inspect the results with common tools
-   such as [QuPath](https://qupath.github.io/) and Python Notebooks.
-   The Launchpad is a user-friendly desktop application running on
-   MacOS X, Windows and Linux that allows you to easily upload your data 
-   without needing to write any code.
-2. Use the **Aignostics CLI** to run AI applications
-   directly from your terminal. The Aignostics Command Line Interface (CLI) allows to query public datasets provided by [NCI Image Data Commons (IDC)](https://portal.imaging.datacommons.cancer.gov/), 
-   run applications on public and private whole slide images, and download results.
-3. Use the included **example** notebook as a starting point to run AI applications
-   directly from your notebook environment. 
-4. Use the **Aignostics Client** to deeply integrate the Aignostics Platform with your enterprise image management systems and scientific workflows.
-   The client makes it easy to call the Aignostics Platform API from your Python codebase.
+1. Use the **Aignostics Launchpad** to analyze whole slide images with AI applications like 
+   [Atlas H&E-TME](https://www.aignostics.com/products/he-tme-profiling-product).
+   This desktop application runs seamlessly on Mac OS X, Windows, and Linux.
+   View your results by launching popular tools such as [QuPath](https://qupath.github.io/) and Python Notebooks with one click.
+2. Use the **Aignostics CLI** to run AI applications directly from your terminal. 
+   This command-line interface lets you query public datasets from the [NCI Image Data Commons (IDC)](https://portal.imaging.datacommons.cancer.gov/),
+   process both public and private whole slide images, and easily download results.
+3. Use the included **example notebooks** as starting points to run AI applications
+   directly from your preferred notebook environment.
+4. Use the **Aignostics Client** to seamlessly integrate the Aignostics Platform with your enterprise image management systems and scientific workflows.
+   The client provides a simple way to access the Aignostics Platform API from your Python codebase.
 
 ### We take quality and security seriously
 
@@ -174,15 +174,14 @@ more about how we achieve
 [operational excellence](https://aignostics.readthedocs.io/en/latest/operational_excellence.html) and
 [security](https://aignostics.readthedocs.io/en/latest/security.html).
 
-## Aignostics Launchpad: Run your first AI workflow in 10 minutes from your Desktop
+## Aignostics Launchpad: Run your first AI analysis in minutes from your desktop
 
-1. Go to [Quick Start](https://platform.aignostics.com/getting-started/quick-start)
-in the Web Console of the Aignostics Platform. 
-2. Copy and paste the install script into your terminal - we support MacOS, Windows and Linux. 
-This will install the [uv package manager](https://github.com/astral-sh/uv) and this
-Python SDK.
-3. Execute `uvx aignostics launchpad` to open the included desktop application.
-4. Follow the instructions in the application to run your first AI workflow.
+1. Visit the [Quick Start](https://platform.aignostics.com/getting-started/quick-start) 
+   page in the Aignostics Platform Web Console.
+2. Copy the installation script and paste it into your terminal - compatible with MacOS, Windows, and Linux.
+3. Launch the application by running `uvx aignostics launchpad`.
+4. Follow the intuitive graphical interface to analyze public datasets or your own whole slide images 
+   with [Atlas H&E-TME](https://www.aignostics.com/products/he-tme-profiling-product) and other AI applications.
 
 ## Aignostics CLI: Manage datasets and application runs from your terminal
 

{aignostics-0.2.0 → aignostics-0.2.1}/README.md

@@ -14,7 +14,8 @@
 [![Uptime](https://uptime.betterstack.com/status-badges/v2/monitor/1wbqa.svg)](https://aignostics.betteruptime.com)
 
 > [!NOTE]
-> This project is currently in alpha phase. Watch or star the repository to stay updated on its progress.
+> The Aignostics Python SDK is in alpha, with [Atlas H&E-TME](https://www.aignostics.com/products/he-tme-profiling-product) running on the [Aignostics Platform](https://platform.aignostics.com) being in [early access](https://www.linkedin.com/posts/aignostics_introducing-atlas-he-tme-aignostics-is-activity-7325865745827979265-Sya9?utm_source=share&utm_medium=member_desktop&rcm=ACoAABRmV7cBCGv8eM_ot_kRTrBsb12olQvoLS4). 
+> Watch or star this repository to receive updates on new features and improvements of the Aignostics Python SDK.
 
 ---
 
@@ -24,19 +25,17 @@
 The Aignostics Python SDK includes multiple pathways to interact with the
 Aignostics Platform:
 
-1. Use the **Aignostics Launchpad** to analyze your whole slide images 
-   with our AI applications and inspect the results with common tools
-   such as [QuPath](https://qupath.github.io/) and Python Notebooks.
-   The Launchpad is a user-friendly desktop application running on
-   MacOS X, Windows and Linux that allows you to easily upload your data 
-   without needing to write any code.
-2. Use the **Aignostics CLI** to run AI applications
-   directly from your terminal. The Aignostics Command Line Interface (CLI) allows to query public datasets provided by [NCI Image Data Commons (IDC)](https://portal.imaging.datacommons.cancer.gov/), 
-   run applications on public and private whole slide images, and download results.
-3. Use the included **example** notebook as a starting point to run AI applications
-   directly from your notebook environment. 
-4. Use the **Aignostics Client** to deeply integrate the Aignostics Platform with your enterprise image management systems and scientific workflows.
-   The client makes it easy to call the Aignostics Platform API from your Python codebase.
+1. Use the **Aignostics Launchpad** to analyze whole slide images with AI applications like 
+   [Atlas H&E-TME](https://www.aignostics.com/products/he-tme-profiling-product).
+   This desktop application runs seamlessly on Mac OS X, Windows, and Linux.
+   View your results by launching popular tools such as [QuPath](https://qupath.github.io/) and Python Notebooks with one click.
+2. Use the **Aignostics CLI** to run AI applications directly from your terminal. 
+   This command-line interface lets you query public datasets from the [NCI Image Data Commons (IDC)](https://portal.imaging.datacommons.cancer.gov/),
+   process both public and private whole slide images, and easily download results.
+3. Use the included **example notebooks** as starting points to run AI applications
+   directly from your preferred notebook environment.
+4. Use the **Aignostics Client** to seamlessly integrate the Aignostics Platform with your enterprise image management systems and scientific workflows.
+   The client provides a simple way to access the Aignostics Platform API from your Python codebase.
 
 ### We take quality and security seriously
 
@@ -58,15 +57,14 @@ more about how we achieve
 [operational excellence](https://aignostics.readthedocs.io/en/latest/operational_excellence.html) and
 [security](https://aignostics.readthedocs.io/en/latest/security.html).
 
-## Aignostics Launchpad: Run your first AI workflow in 10 minutes from your Desktop
+## Aignostics Launchpad: Run your first AI analysis in minutes from your desktop
 
-1. Go to [Quick Start](https://platform.aignostics.com/getting-started/quick-start)
-in the Web Console of the Aignostics Platform. 
-2. Copy and paste the install script into your terminal - we support MacOS, Windows and Linux. 
-This will install the [uv package manager](https://github.com/astral-sh/uv) and this
-Python SDK.
-3. Execute `uvx aignostics launchpad` to open the included desktop application.
-4. Follow the instructions in the application to run your first AI workflow.
+1. Visit the [Quick Start](https://platform.aignostics.com/getting-started/quick-start) 
+   page in the Aignostics Platform Web Console.
+2. Copy the installation script and paste it into your terminal - compatible with MacOS, Windows, and Linux.
+3. Launch the application by running `uvx aignostics launchpad`.
+4. Follow the intuitive graphical interface to analyze public datasets or your own whole slide images 
+   with [Atlas H&E-TME](https://www.aignostics.com/products/he-tme-profiling-product) and other AI applications.
 
 ## Aignostics CLI: Manage datasets and application runs from your terminal
 

{aignostics-0.2.0 → aignostics-0.2.1}/examples/notebook.py

@@ -2,7 +2,7 @@
 # requires-python = ">=3.13"
 # dependencies = [
 #     "marimo",
-#     "aignostics==0.2.0",
+#     "aignostics==0.2.1",
 # ]
 # ///
 

{aignostics-0.2.0 → aignostics-0.2.1}/pyproject.toml

@@ -1,15 +1,26 @@
 [project]
 name = "aignostics"
-version = "0.2.0"
+version = "0.2.1"
 description = "🔬 Python SDK providing access to Aignostics AI services."
 readme = "README.md"
 authors = [
     { name = "Helmut Hoffer von Ankershoffen", email = "helmut@aignostics.com" },
+    { name = "Andreas Kuhn" },
 ]
 license = { file = "LICENSE" }
 
 keywords = [
     "aignostics",
+    "atlas",
+    "whole-slide-imaging",
+    "machine-learning",
+    "digital-pathology",
+    "medical-imaging",
+    "qupath",
+    "dicom",
+    "pydicom",
+    "openslide",
+    "image-data-commons",
     "act",
     "codecov",
     "copier",
@@ -36,7 +47,6 @@ keywords = [
     "sonarqube",
     "sonarcloud",
     "sphinx",
-    "streamlit",
     "typer",
     "uv",
 ]
@@ -126,7 +136,7 @@ dependencies = [
 jupyter = ["jupyter>=1.1.1"]
 marimo = [
     "cloudpathlib>=0.21.1",
-    "marimo>=0.13.10",
+    "marimo>=0.13.11",
     "matplotlib>=3.10.3",
     "shapely>=2.1.0",
 ]
@@ -146,7 +156,7 @@ dev = [
     "pip-audit>=2.9.0",
     "pip-licenses @ git+https://github.com/neXenio/pip-licenses.git@master", # https://github.com/raimon49/pip-licenses/pull/224
     "pre-commit>=4.1.0",
-    "pyright>=1.1.399",
+    "pyright>=1.1.401",
     "pytest>=8.3.5",
     "pytest-asyncio>=0.26.0",
     "pytest-cov>=6.1.1",
@@ -344,7 +354,7 @@ source = ["src/"]
 
 
 [tool.bumpversion]
-current_version = "0.2.0"
+current_version = "0.2.1"
 parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
 serialize = ["{major}.{minor}.{patch}"]
 search = "{current_version}"
@@ -372,6 +382,14 @@ post_commit_hooks = []
 
 [[tool.bumpversion.files]]
 filename = "pyproject.toml"
+search = """
+[project]
+name = \"aignostics\"
+version = \"{current_version}\""""
+replace = """
+[project]
+name = \"aignostics\"
+version = \"{new_version}\""""
 
 [[tool.bumpversion.files]]
 filename = "VERSION"
@@ -401,11 +419,11 @@ header = """
 body = """
 
 {%- macro remote_url() -%}
-  https://github.com/{{ remote.github.owner }}/{{ remote.github.repo }}
+https://github.com/{{ remote.github.owner }}/{{ remote.github.repo }}
 {%- endmacro -%}
 
 {% macro print_commit(commit) -%}
-    - {% if commit.scope %}*({{ commit.scope }})* {% endif %}\
+- {% if commit.scope %}*({{ commit.scope }})* {% endif %}\
         {% if commit.breaking %}[**breaking**] {% endif %}\
         {{ commit.message | upper_first }} - \
         ([{{ commit.id | truncate(length=7, end="") }}]({{ self::remote_url() }}/commit/{{ commit.id }}))\
@@ -413,17 +431,14 @@ body = """
 
 {% if version %}\
     {% if previous.version %}\
-        ## [{{ version | trim_start_matches(pat="v") }}]\
           ({{ self::remote_url() }}/compare/{{ previous.version }}..{{ version }}) - {{ timestamp | date(format="%Y-%m-%d") }}
     {% else %}\
-        ## [{{ version | trim_start_matches(pat="v") }}] - {{ timestamp | date(format="%Y-%m-%d") }}
     {% endif %}\
 {% else %}\
-    ## [unreleased]
+
 {% endif %}\
 
 {% for group, commits in commits | group_by(attribute="group") %}
-    ### {{ group | striptags | trim | upper_first }}
     {% for commit in commits
     | unique(attribute="message")
     | filter(attribute="scope")
@@ -439,12 +454,12 @@ body = """
 {% endfor -%}
 {%- if github -%}
 {% if github.contributors | filter(attribute="is_first_time", value=true) | length != 0 %}
-  ## New Contributors ❤️
+
 {% endif %}\
 {% for contributor in github.contributors | filter(attribute="is_first_time", value=true) %}
   * @{{ contributor.username }} made their first contribution
     {%- if contributor.pr_number %} in \
-      [#{{ contributor.pr_number }}]({{ self::remote_url() }}/pull/{{ contributor.pr_number }}) \
+[#{{ contributor.pr_number }}]({{ self::remote_url() }}/pull/{{ contributor.pr_number }}) \
     {%- endif %}
 {%- endfor -%}
 {%- endif %}
@@ -455,6 +470,11 @@ body = """
 footer = """
 """
 
+## [{{ version | trim_start_matches(pat="v") }}]\
+## [{{ version | trim_start_matches(pat="v") }}] - {{ timestamp | date(format="%Y-%m-%d") }}
+## [unreleased]
+### {{ group | striptags | trim | upper_first }}
+## New Contributors ❤️
 ## [{{ version | trim_start_matches(pat="v") }}]\
 ## [{{ version | trim_start_matches(pat="v") }}] - {{ timestamp | date(format="%Y-%m-%d") }}
 ## [unreleased]